Package: ECOTOXr 1.2.4

ECOTOXr: Download and Extract Data from US EPA's ECOTOX Database

The US EPA ECOTOX database is a freely available database with a treasure of aquatic and terrestrial ecotoxicological data. As the online search interface doesn't come with an API, this package provides the means to easily access and search the database in R. To this end, all raw tables are downloaded from the EPA website and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.

Authors:Pepijn de Vries [aut, cre, dtc]

ECOTOXr_1.2.4.tar.gz
ECOTOXr_1.2.4.zip(r-4.7)ECOTOXr_1.2.4.zip(r-4.6)ECOTOXr_1.2.4.zip(r-4.5)
ECOTOXr_1.2.4.tgz(r-4.6-any)ECOTOXr_1.2.4.tgz(r-4.5-any)
ECOTOXr_1.2.4.tar.gz(r-4.7-any)ECOTOXr_1.2.4.tar.gz(r-4.6-any)
ECOTOXr_1.2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ECOTOXr/json (API)

# Install 'ECOTOXr' in R:
install.packages('ECOTOXr', repos = c('https://pepijn-devries.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pepijn-devries/ecotoxr/issues

Pkgdown/docs site:https://pepijn-devries.github.io

On CRAN:

Conda:

datadatabase

6.03 score 15 stars 12 scripts 344 downloads 30 exports 54 dependencies

Last updated from:3145f3ede5 (on main). Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK172
source / vignettesOK209
linux-release-x86_64OK163
macos-release-arm64OK113
macos-oldrel-arm64OK139
windows-develOK135
windows-releaseOK110
windows-oldrelOK108
wasm-releaseOK121

Exports:as_date_ecotoxas_numeric_ecotoxas_unit_ecotoxas.casbuild_ecotox_sqlitecascheck_ecotox_availabilitycheck_ecotox_buildcheck_ecotox_versioncite_ecotoxdbConnectEcotoxdbDisconnectEcotoxdownload_ecotox_dataget_ecotox_infoget_ecotox_pathget_ecotox_sqlite_fileget_ecotox_urlis.caslist_ecotox_fieldslist_ecotox_web_fieldsmixed_to_single_unitprocess_ecotox_datesprocess_ecotox_numericsprocess_ecotox_unitssearch_ecotoxsearch_ecotox_lazysearch_query_ecotoxshow.caswebsearch_comptoxwebsearch_ecotox

Dependencies:askpassbitbit64blobcachemcellrangerclicliprcpp11crayoncurlDBIdbplyrdplyrfastmapgenericsgluehmshttrhttr2jsonlitelifecyclemagrittrmemoisemimeopensslpillarpkgconfigprettyunitsprogresspurrrR6rappdirsRcppreadrreadxlrematchrlangRSQLitervestselectrstringistringrsystibbletidyrtidyselecttzdbunitsutf8vctrsvroomwithrxml2

Sanitising ECOTOX
Sanitising units | Consequences of unit sanitation | Sanitising numerics | Consequences of numeric sanitation | Combining numerics with units | Sanitising dates
Rendered fromsanitising-ecotox.Rmdusingknitr::rmarkdown

Last update: 2025-09-24
Started: 2025-03-11

Searching ECOTOX
Searching the local database | Three ways of querying the local database | The curious case of chemical CAS numbers | Searching the online database
Rendered fromsearching-ecotox.Rmdusingknitr::rmarkdown

Last update: 2025-08-18
Started: 2025-02-12

ECOTOX database schema
The database's relational structure | Setting up queries: some examples | All test results for tests carried out with Insecta | A random substance and random species | Dose information | Automatically generating queries | Overview of tables and fields
Rendered fromecotox-schema.Rmdusingknitr::rmarkdown

Last update: 2025-02-19
Started: 2025-02-16

Reproducibility
Rules of thumb
Rendered fromreproducibility.Rmdusingknitr::rmarkdown

Last update: 2025-02-19
Started: 2025-02-19

Readme and manuals

Help Manual

Help pageTopics
Values represented by ECOTOX 'character' to datesas_date_ecotox
Values represented by ECOTOX 'character' to 'numeric'as_numeric_ecotox
Text from the ECOTOX database to 'mixed_units'as_unit_ecotox
Build an SQLite database from zip archived tables downloaded from EPA websitebuild_ecotox_sqlite
Functions for handling chemical abstract service (CAS) registry numbersas.cas as.character.cas as.data.frame.cas as.double.cas as.integer.cas as.list.cas c.cas cas format.cas is.cas print.cas show.cas [.cas [<-.cas [[.cas [[<-.cas
Check whether a ECOTOX database exists locallycheck_ecotox_availability
Check the locally build database for validitycheck_ecotox_build
Check if the locally build database is up to datecheck_ecotox_version
Cite the downloaded copy of the ECOTOX databasecite_ecotox
Open or close a connection to the local ECOTOX databasedbConnectEcotox dbDisconnectEcotox
Download and extract ECOTOX database files and compose databasedownload_ecotox_data
Get information on the local ECOTOX database when availableget_ecotox_info
The local path to the ECOTOX database (directory or sqlite file)get_ecotox_path get_ecotox_sqlite_file
Get ECOTOX download URL from EPA websiteget_ecotox_url
List the field names that are available from the ECOTOX databaselist_ecotox_fields
Convert mixed units to a specific unitmixed_to_single_unit
Process ECOTOX search results by converting 'character' to dates where relevantprocess_ecotox_dates
Process ECOTOX search results by converting 'character' to 'numeric' where relevantprocess_ecotox_numerics
Process ECOTOX search results by converting 'character' to units where relevantprocess_ecotox_units
Search and retrieve toxicity records from the databasesearch_ecotox search_ecotox_lazy search_query_ecotox
Search and retrieve substance information from <https://comptox.epa.gov/dashboard>websearch_comptox
Search and retrieve toxicity records from the online databaselist_ecotox_web_fields websearch_ecotox